{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Andrew Kjar"],"organism":["Homo sapiens"],"software":["Rsubread (2.18.0)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16510"],"description":["Developing and benchmarking model systems to understand neurodegeneration remains an important challenge. In this work, we overexpressed mutant MAPT (P301L,V337M) in neural organoids to understand the resulting pathology."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - NGS sequencing was performed via paired-end 150 bp on an Illumina NovaSeq X Plus with a targeted 50 million reads per sample.","Nucleic Acid Extraction - RNA samples were extracted using the QIAGEN RNeasy micro plus kit.","Library Construction - Purified RNA samples were submitted to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core for bulk sequencing. cDNA libraries were prepared with a stranded mRNA (polyA-selected) library preparation kit.","Sample Collection - Day 90 organoids were collected from culture media, washed in PBS, and then homogenized in RLT buffer with BME."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Paired-end bulk RNA-seq reads were obtained as gzipped FASTQ files.  Reads were aligned to the human reference genome (hg38) using an RNA-seq–specific alignment mode with paired-end information enabled (Rsubread). Aligned BAM files were collected and quantified at the gene level using the featureCounts function. Raw counts were uploaded as the processed file."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["N/A","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Andrew Kjar"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA sequencing of mutant MAPT over-expression in neural organoids","description":"Developing and benchmarking model systems to understand neurodegeneration remains an important challenge. In this work, we overexpressed mutant MAPT (P301L,V337M) in neural organoids to understand the resulting pathology.","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T01:03:46.789Z","creation":"2026-01-02T16:00:28.544Z"},"accession":"E-MTAB-16510","cross_references":{"ENA":["ERP187229"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}